From df60bf2a50e21881e975b74efe9b967b74e990fc Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 27 Jan 2021 11:10:48 +0100
Subject: [PATCH] src/nt_composition/__main__.py: add inflation parameter
---
src/nt_composition/__main__.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/src/nt_composition/__main__.py b/src/nt_composition/__main__.py
index 9b0bd118..a6c34da3 100644
--- a/src/nt_composition/__main__.py
+++ b/src/nt_composition/__main__.py
@@ -21,7 +21,8 @@ import lazyparser as lp
def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt',
same_gene: bool = False, compute_mean: bool = True,
iteration: int = 10000, kind: str = 'density',
- community_size: int = -1, inter_chr: bool = False,
+ community_size: int = -1, inflation: float = 1.5,
+ inter_chr: bool = False,
level: str = "exon",
logging_level: str = "DISABLE"):
"""
@@ -47,6 +48,8 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt',
randomly expected. (default : 'density').*
:param community_size: consider only exons within communities bigger \
than community size. if community_size = -1. This option is deactivated.
+ :param inflation: The inflation parameter. This parameter is used only \
+ if community size is not -1. (default 1.5).
:param inter_chr: True to only get inter-chromosomal interactions \
False else (default: False)
:param level: The kind of feature to analyse (exon or gene)
@@ -57,9 +60,9 @@ def launcher(weight: int = 1, global_weight: int = 0, ft_type: str = 'nt',
community_size = None
if kind == "density":
create_all_frequency_figures(ConfigNt.cpu, weight, global_weight,
- ft_type, same_gene, compute_mean,
- community_size, inter_chr, level,
- logging_level)
+ ft_type, same_gene, inflation,
+ compute_mean, community_size, inter_chr,
+ level, logging_level)
else:
create_all_distance_figures(ConfigNt.cpu, weight, global_weight,
ft_type, same_gene, iteration, inter_chr,
--
GitLab